//
// Manta - Structural Variant and Indel Caller
// Copyright (c) 2013-2019 Illumina, Inc.
//
// This program is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// at your option) any later version.
//
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program.  If not, see <http://www.gnu.org/licenses/>.
//
//

/// \file
/// \author Chris Saunders
///

#pragma once

#include "common/Program.hpp"
#include "manta/SVLocusScanner.hpp"
#include "options/AlignmentFileOptions.hpp"
#include "options/ReadScannerOptions.hpp"
#include "options/SVLocusSetOptions.hpp"

#include <vector>

struct ESLOptions {
  ESLOptions() : graphOpt(SVObservationWeights::observation)  // initialize noise edge filtration parameters
  {
  }

  AlignmentFileOptions alignFileOpt;
  ReadScannerOptions   scanOpt;
  SVLocusSetOptions    graphOpt;

  std::string              referenceFilename;
  std::string              outputFilename;
  std::vector<std::string> regions;
  std::string              statsFilename;
  std::string              chromDepthFilename;

  /// TODO remove the need for this bool by having a single overlap pair handler
  bool isRNA = false;
};

void parseESLOptions(const illumina::Program& prog, int argc, char* argv[], ESLOptions& opt);
